[2024-01-25 19:52:05,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:05,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:05,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ecb57a9-9781-46a3-a116-bd5eebf463cf/dqc_reference
[2024-01-25 19:52:06,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:06,861] [INFO] Task started: Prodigal
[2024-01-25 19:52:06,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg1141ee12-5158-48a0-9f21-7de2588f205e/GCF_900461555.1_51485_A02_genomic.fna.gz | prodigal -d GCF_900461555.1_51485_A02_genomic.fna/cds.fna -a GCF_900461555.1_51485_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:14,360] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:14,361] [INFO] Task started: HMMsearch
[2024-01-25 19:52:14,361] [INFO] Running command: hmmsearch --tblout GCF_900461555.1_51485_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ecb57a9-9781-46a3-a116-bd5eebf463cf/dqc_reference/reference_markers.hmm GCF_900461555.1_51485_A02_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:14,642] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:14,643] [INFO] Found 6/6 markers.
[2024-01-25 19:52:14,672] [INFO] Query marker FASTA was written to GCF_900461555.1_51485_A02_genomic.fna/markers.fasta
[2024-01-25 19:52:14,673] [INFO] Task started: Blastn
[2024-01-25 19:52:14,673] [INFO] Running command: blastn -query GCF_900461555.1_51485_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ecb57a9-9781-46a3-a116-bd5eebf463cf/dqc_reference/reference_markers.fasta -out GCF_900461555.1_51485_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:15,276] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:15,279] [INFO] Selected 10 target genomes.
[2024-01-25 19:52:15,279] [INFO] Target genome list was writen to GCF_900461555.1_51485_A02_genomic.fna/target_genomes.txt
[2024-01-25 19:52:15,315] [INFO] Task started: fastANI
[2024-01-25 19:52:15,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg1141ee12-5158-48a0-9f21-7de2588f205e/GCF_900461555.1_51485_A02_genomic.fna.gz --refList GCF_900461555.1_51485_A02_genomic.fna/target_genomes.txt --output GCF_900461555.1_51485_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:23,461] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:23,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ecb57a9-9781-46a3-a116-bd5eebf463cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:23,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ecb57a9-9781-46a3-a116-bd5eebf463cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:23,468] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:52:23,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:23,468] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Legionella quinlivanii	strain=NCTC12433	GCA_900461555.1	45073	45073	type	True	100.0	1201	1202	95	conclusive
Legionella quinlivanii	strain=DSM 21216	GCA_900108145.1	45073	45073	type	True	99.9602	1158	1202	95	conclusive
Legionella quinlivanii	strain=CDC#1442-AUS-E	GCA_001467975.1	45073	45073	type	True	99.9501	1174	1202	95	conclusive
Legionella quinlivanii	strain=1442-AUS-E	GCA_900639995.1	45073	45073	type	True	99.9372	1141	1202	95	conclusive
Legionella birminghamensis	strain=1407-AL-H	GCA_900639775.1	28083	28083	type	True	80.4809	559	1202	95	below_threshold
Legionella sainthelensi	strain=Mt.St.Helens-4	GCA_001468105.1	28087	28087	type	True	77.9358	55	1202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:23,469] [INFO] DFAST Taxonomy check result was written to GCF_900461555.1_51485_A02_genomic.fna/tc_result.tsv
[2024-01-25 19:52:23,470] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:23,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:23,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ecb57a9-9781-46a3-a116-bd5eebf463cf/dqc_reference/checkm_data
[2024-01-25 19:52:23,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:23,507] [INFO] Task started: CheckM
[2024-01-25 19:52:23,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900461555.1_51485_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900461555.1_51485_A02_genomic.fna/checkm_input GCF_900461555.1_51485_A02_genomic.fna/checkm_result
[2024-01-25 19:52:51,024] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:51,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:51,041] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:51,042] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:51,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900461555.1_51485_A02_genomic.fna/markers.fasta)
[2024-01-25 19:52:51,042] [INFO] Task started: Blastn
[2024-01-25 19:52:51,042] [INFO] Running command: blastn -query GCF_900461555.1_51485_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ecb57a9-9781-46a3-a116-bd5eebf463cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_900461555.1_51485_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:52,117] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:52,120] [INFO] Selected 15 target genomes.
[2024-01-25 19:52:52,120] [INFO] Target genome list was writen to GCF_900461555.1_51485_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:52,157] [INFO] Task started: fastANI
[2024-01-25 19:52:52,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg1141ee12-5158-48a0-9f21-7de2588f205e/GCF_900461555.1_51485_A02_genomic.fna.gz --refList GCF_900461555.1_51485_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900461555.1_51485_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:02,313] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:02,322] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:02,323] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900461555.1	s__Legionella_C quinlivanii	100.0	1201	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.97	99.95	0.99	0.98	4	conclusive
GCF_003265995.1	s__Legionella_C quinlivanii_A	92.1613	1079	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	96.16	96.16	0.91	0.91	2	-
GCF_900452515.1	s__Legionella_C birminghamensis	80.7237	567	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.98	99.98	1.00	1.00	3	-
GCF_900637685.1	s__Legionella sainthelensi	78.5194	58	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.79	95.71	0.95	0.89	8	-
GCF_000953635.1	s__Tatlockia micdadei	78.395	72	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.75	0.99	0.96	7	-
GCF_900452865.1	s__Legionella_C taurinensis	78.1388	94	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.63	99.52	0.96	0.95	16	-
GCF_900452385.1	s__Tatlockia donaldsonii	77.9848	80	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467615.1	s__Legionella_C erythra	77.2855	100	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.95	99.95	0.98	0.98	2	-
GCF_000756815.1	s__Tatlockia massiliensis	77.2686	89	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001465875.1	s__Legionella saoudiensis	77.2268	65	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468125.1	s__Legionella_C rubrilucens	77.1761	92	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000701265.1	s__Legionella wadsworthii	77.0037	64	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	1.00	0.99	3	-
GCA_013812775.1	s__Tatlockia sp013812775	76.7109	60	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:02,324] [INFO] GTDB search result was written to GCF_900461555.1_51485_A02_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:02,325] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:02,328] [INFO] DFAST_QC result json was written to GCF_900461555.1_51485_A02_genomic.fna/dqc_result.json
[2024-01-25 19:53:02,328] [INFO] DFAST_QC completed!
[2024-01-25 19:53:02,329] [INFO] Total running time: 0h0m57s